Literature DB >> 29038113

Will Systems Biology Deliver Its Promise and Contribute to the Development of New or Improved Vaccines? From Data to Understanding through Systems Biology.

Thomas Hagan1,2, Bali Pulendran1,2.   

Abstract

The advent of high-throughput "omics" technologies, combined with the computational and statistical methods necessary to analyze such data, have revolutionized biology, enabling a global view of the complex molecular processes and interactions that occur within a biological system. Such systems-based approaches have begun to be used in the evaluation of immune responses to vaccination, with the promise of identifying predictive biomarkers capable of rapidly evaluating vaccine efficacy, transforming our understanding of the immune mechanisms responsible for protective responses to vaccination and contributing to a new generation of rationally designed vaccines. Here we present our opinion that systems biology does indeed have a critical role in the future of vaccinology. Such approaches have shown potential in identifying transcriptional and cellular signatures of responsiveness to vaccination using diverse vaccines, adjuvants, and human populations. These findings, coupled with further mechanistic evaluation in animal models, will guide development of targeted vaccine and adjuvant formulations designed to optimally induce protective responses in populations of differing immune status.
Copyright © 2018 Cold Spring Harbor Laboratory Press; all rights reserved.

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Year:  2018        PMID: 29038113      PMCID: PMC5902663          DOI: 10.1101/cshperspect.a028894

Source DB:  PubMed          Journal:  Cold Spring Harb Perspect Biol        ISSN: 1943-0264            Impact factor:   10.005


  54 in total

1.  Systems Analysis of Immunity to Influenza Vaccination across Multiple Years and in Diverse Populations Reveals Shared Molecular Signatures.

Authors:  Helder I Nakaya; Thomas Hagan; Sai S Duraisingham; Eva K Lee; Marcin Kwissa; Nadine Rouphael; Daniela Frasca; Merril Gersten; Aneesh K Mehta; Renaud Gaujoux; Gui-Mei Li; Shakti Gupta; Rafi Ahmed; Mark J Mulligan; Shai Shen-Orr; Bonnie B Blomberg; Shankar Subramaniam; Bali Pulendran
Journal:  Immunity       Date:  2015-12-15       Impact factor: 31.745

Review 2.  Immunological mechanisms of vaccination.

Authors:  Bali Pulendran; Rafi Ahmed
Journal:  Nat Immunol       Date:  2011-06       Impact factor: 25.606

Review 3.  Systems biology of vaccination in the elderly.

Authors:  Sai S Duraisingham; Nadine Rouphael; Mary M Cavanagh; Helder I Nakaya; Jorg J Goronzy; Bali Pulendran
Journal:  Curr Top Microbiol Immunol       Date:  2013       Impact factor: 4.291

Review 4.  Systems vaccinology: Enabling rational vaccine design with systems biological approaches.

Authors:  Thomas Hagan; Helder I Nakaya; Shankar Subramaniam; Bali Pulendran
Journal:  Vaccine       Date:  2015-04-06       Impact factor: 3.641

5.  Multisite comparison of high-sensitivity multiplex cytokine assays.

Authors:  Elizabeth Crabb Breen; Sandra M Reynolds; Christopher Cox; Lisa P Jacobson; Larry Magpantay; Candice B Mulder; Oliver Dibben; Joseph B Margolick; Jay H Bream; Elise Sambrano; Otoniel Martínez-Maza; Elizabeth Sinclair; Persephone Borrow; Alan L Landay; Charles R Rinaldo; Philip J Norris
Journal:  Clin Vaccine Immunol       Date:  2011-06-22

6.  Variation in the human immune system is largely driven by non-heritable influences.

Authors:  Petter Brodin; Vladimir Jojic; Tianxiang Gao; Sanchita Bhattacharya; Cesar J Lopez Angel; David Furman; Shai Shen-Orr; Cornelia L Dekker; Gary E Swan; Atul J Butte; Holden T Maecker; Mark M Davis
Journal:  Cell       Date:  2015-01-15       Impact factor: 41.582

Review 7.  Malaria vaccine development: persistent challenges.

Authors:  Ashley M Vaughan; Stefan H I Kappe
Journal:  Curr Opin Immunol       Date:  2012-04-21       Impact factor: 7.486

Review 8.  Systems vaccinology.

Authors:  Bali Pulendran; Shuzhao Li; Helder I Nakaya
Journal:  Immunity       Date:  2010-10-29       Impact factor: 31.745

9.  Human circulating PD-1+CXCR3-CXCR5+ memory Tfh cells are highly functional and correlate with broadly neutralizing HIV antibody responses.

Authors:  Michela Locci; Colin Havenar-Daughton; Elise Landais; Jennifer Wu; Mark A Kroenke; Cecilia L Arlehamn; Laura F Su; Rafael Cubas; Mark M Davis; Alessandro Sette; Elias K Haddad; Pascal Poignard; Shane Crotty
Journal:  Immunity       Date:  2013-09-12       Impact factor: 31.745

10.  Systems biology of vaccination for seasonal influenza in humans.

Authors:  Helder I Nakaya; Jens Wrammert; Eva K Lee; Luigi Racioppi; Stephanie Marie-Kunze; W Nicholas Haining; Anthony R Means; Sudhir P Kasturi; Nooruddin Khan; Gui-Mei Li; Megan McCausland; Vibhu Kanchan; Kenneth E Kokko; Shuzhao Li; Rivka Elbein; Aneesh K Mehta; Alan Aderem; Kanta Subbarao; Rafi Ahmed; Bali Pulendran
Journal:  Nat Immunol       Date:  2011-07-10       Impact factor: 25.606

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  19 in total

Review 1.  Applications of mechanistic modelling to clinical and experimental immunology: an emerging technology to accelerate immunotherapeutic discovery and development.

Authors:  L V Brown; E A Gaffney; J Wagg; M C Coles
Journal:  Clin Exp Immunol       Date:  2018-09       Impact factor: 4.330

Review 2.  The dawn of vaccines for cancer prevention.

Authors:  Olivera J Finn
Journal:  Nat Rev Immunol       Date:  2017-12-27       Impact factor: 53.106

3.  Antibiotics-Driven Gut Microbiome Perturbation Alters Immunity to Vaccines in Humans.

Authors:  Thomas Hagan; Mario Cortese; Nadine Rouphael; Carolyn Boudreau; Caitlin Linde; Mohan S Maddur; Jishnu Das; Hong Wang; Jenna Guthmiller; Nai-Ying Zheng; Min Huang; Amit A Uphadhyay; Luiz Gardinassi; Caroline Petitdemange; Michele Paine McCullough; Sara Jo Johnson; Kiran Gill; Barbara Cervasi; Jun Zou; Alexis Bretin; Megan Hahn; Andrew T Gewirtz; Steve E Bosinger; Patrick C Wilson; Shuzhao Li; Galit Alter; Surender Khurana; Hana Golding; Bali Pulendran
Journal:  Cell       Date:  2019-09-05       Impact factor: 41.582

4.  Tracking immunodynamics by identification of S-G2/M-phase T cells in human peripheral blood.

Authors:  Miguel Muñoz-Ruiz; Irma Pujol-Autonell; Hefin Rhys; Heather M Long; Maria Greco; Mark Peakman; Tim Tree; Adrian C Hayday; Francesca Di Rosa
Journal:  J Autoimmun       Date:  2020-05-12       Impact factor: 7.094

5.  Genome-wide association study of individual differences of human lymphocyte profiles using large-scale cytometry data.

Authors:  Daigo Okada; Naotoshi Nakamura; Kazuya Setoh; Takahisa Kawaguchi; Koichiro Higasa; Yasuharu Tabara; Fumihiko Matsuda; Ryo Yamada
Journal:  J Hum Genet       Date:  2020-11-23       Impact factor: 3.172

6.  Clinical Protocol for a Longitudinal Cohort Study Employing Systems Biology to Identify Markers of Vaccine Immunogenicity in Newborn Infants in The Gambia and Papua New Guinea.

Authors:  Olubukola T Idoko; Kinga K Smolen; Oghenebrume Wariri; Abdulazeez Imam; Casey P Shannon; Tida Dibassey; Joann Diray-Arce; Alansana Darboe; Julia Strandmark; Rym Ben-Othman; Oludare A Odumade; Kerry McEnaney; Nelly Amenyogbe; William S Pomat; Simon van Haren; Guzmán Sanchez-Schmitz; Ryan R Brinkman; Hanno Steen; Robert E W Hancock; Scott J Tebbutt; Peter C Richmond; Anita H J van den Biggelaar; Tobias R Kollmann; Ofer Levy; Al Ozonoff; Beate Kampmann
Journal:  Front Pediatr       Date:  2020-04-30       Impact factor: 3.418

Review 7.  Systems vaccinology and big data in the vaccine development chain.

Authors:  René H M Raeven; Elly van Riet; Hugo D Meiring; Bernard Metz; Gideon F A Kersten
Journal:  Immunology       Date:  2018-11-13       Impact factor: 7.397

8.  A system-view of Bordetella pertussis booster vaccine responses in adults primed with whole-cell versus acellular vaccine in infancy.

Authors:  Ricardo da Silva Antunes; Ferran Soldevila; Mikhail Pomaznoy; Mariana Babor; Jason Bennett; Yuan Tian; Natalie Khalil; Yu Qian; Aishwarya Mandava; Richard H Scheuermann; Mario Cortese; Bali Pulendran; Christopher D Petro; Adrienne P Gilkes; Lisa A Purcell; Alessandro Sette; Bjoern Peters
Journal:  JCI Insight       Date:  2021-04-08

9.  BALDR: a computational pipeline for paired heavy and light chain immunoglobulin reconstruction in single-cell RNA-seq data.

Authors:  Amit A Upadhyay; Robert C Kauffman; Amber N Wolabaugh; Alice Cho; Nirav B Patel; Samantha M Reiss; Colin Havenar-Daughton; Reem A Dawoud; Gregory K Tharp; Iñaki Sanz; Bali Pulendran; Shane Crotty; F Eun-Hyung Lee; Jens Wrammert; Steven E Bosinger
Journal:  Genome Med       Date:  2018-03-20       Impact factor: 15.266

10.  Systemic IL-15, IFN-γ, and IP-10/CXCL10 signature associated with effective immune response to SARS-CoV-2 in BNT162b2 mRNA vaccine recipients.

Authors:  Cristina Bergamaschi; Evangelos Terpos; Margherita Rosati; Matthew Angel; Jenifer Bear; Dimitris Stellas; Sevasti Karaliota; Filia Apostolakou; Tina Bagratuni; Dimitris Patseas; Sentiljana Gumeni; Ioannis P Trougakos; Meletios A Dimopoulos; Barbara K Felber; George N Pavlakis
Journal:  Cell Rep       Date:  2021-07-23       Impact factor: 9.423

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